[gmx-users] rerun warning

[Poojari, Chetan]

Hi Justin,

As I dont have velocities defined in my traj. file, please can I know if theres some possibility of  including them to the traj. file


cheers,
chetan 

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 16 September 2010 12:35
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] rerun warning

Poojari, Chetan wrote:
> Hello Mark,
>
> Thank you very much for quick reply.
>
> I am looking for LJ and coul interactions, please can i know what can be done to avoid these warnings if incase i want to calculate kinetic quantities...
>

You need velocities, and thus, a .trr file.

-Justin

>
> cheers,
> chetan
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [mark.abraham at anu.edu.au]
> Sent: 16 September 2010 12:12
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] rerun warning
>
> ----- Original Message -----
> From: "Poojari, Chetan" <c.poojari at fz-juelich.de>
> Date: Thursday, September 16, 2010 20:04
> Subject: [gmx-users] rerun warning
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>
>> Hi,
>>
>> I am doing  rerun to calculate  LJ-SR & coul-SR
>> interactions and  other energy terms for energygrps defined
>> in mdp file.
>>
>> I have constrained all bonds with lincs algorithm in mdp file.
>>
>> While running rerun i get following warnings........
>>
>> WARNING: Some frames do not contain velocities.
>>          Ekin,
>> temperature and pressure are incorrect,
>>          the virial will
>> be incorrect when constraints are present.
>>
>>
>> Please can I Know if the energy values generated are they
>> incorrect........if so how can i recalculate correct energies as
>> i dont have velocities in my file to use  g_traj
>
> If you're not trying to calculate the kinds of *kinetic* quantities described in the warning, then you don't care. Your first sentence sounds like you're after *static* quantities. If you do want kinetic quantities, then you're in trouble.
>
> Mark
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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